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Hassan BA, Milicaj J, Ramirez-Mondragon CA, Sham YY, Taylor EA. Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes. J Chem Inf Model 2022; 62:324-339. [PMID: 34967618 PMCID: PMC8864558 DOI: 10.1021/acs.jcim.1c00868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Understanding the dynamical motions and ligand recognition motifs of heptosyltransferase I (HepI) can be critical to discerning the behavior of other glycosyltransferase (GT) enzymes. Prior studies in our lab have demonstrated that GTs in the GT-B structural class, which are characterized by their connection of two Rossman-like domains by a linker region, have conserved structural fold and dynamical motions, despite low sequence homology, therefore making discoveries found in HepI transferable to other GT-B enzymes. Through molecular dynamics simulations and ligand binding free energy analysis of HepI in the apo and bound complexes (for all kinetically relevant combinations of the native substrates/products), we have determined the energetically favored enzymatic pathway for ligand binding and release. Our principal component, dynamic cross correlation, and network analyses of the simulations have revealed correlated motions involving residues within the N-terminal domain communicating with C-terminal domain residues via both proximal amino acid residues and also functional groups of the bound substrates. Analyses of the structural changes, energetics of substrate/product binding, and changes in pKa have elucidated a variety of inter and intradomain interactions that are critical for enzyme catalysis. These data corroborate our experimental observations of protein conformational changes observed in both presteady state kinetic and circular dichroism analyses of HepI. These simulations provided invaluable structural insights into the regions involved in HepI conformational rearrangement upon ligand binding. Understanding the specific interactions governing conformational changes is likely to enhance our efforts to develop novel dynamics disrupting inhibitors against GT-B structural enzymes in the future.
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Affiliation(s)
- Bakar A. Hassan
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Carlos Andres Ramirez-Mondragon
- Department of Integrative Biology and Physiology, Medical School and Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yuk Yin Sham
- Department of Integrative Biology and Physiology, Medical School and Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erika A. Taylor
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, Gao J, Taylor EA, Sham YY. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. Int J Mol Sci 2021; 22:ijms22094619. [PMID: 33924837 PMCID: PMC8124905 DOI: 10.3390/ijms22094619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022] Open
Abstract
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and closed conformations of these unbound proteins, respectively, and we sought to identify the major dynamical modes and communication networks that interconnect the open and closed structures. We provide the first reported evidence within the scope of our simulation parameters that the interconversion between open and closed conformations is a hierarchical multistep process which can be a conserved feature of enzymes of the same structural superfamily. Each of these motions involves of a collection of smaller molecular reorientations distributed across both domains, highlighting the complexities of protein dynamic involved in the interconversion process. Additionally, dynamic cross-correlation analysis was employed to explore the potential effect of distal residues on the catalytic efficiency of HepI. Multiple distal nonionizable residues of the C-terminal domain exhibit motions anticorrelated to positively charged residues in the active site in the N-terminal domain involved in substrate binding. Mutations of these residues resulted in a reduction in negatively correlated motions and an altered enzymatic efficiency that is dominated by lower Km values with kcat effectively unchanged. The findings suggest that residues with opposing conformational motions involved in the opening and closing of the bidomain HepI protein can allosterically alter the population and conformation of the “closed” state, essential to the formation of the Michaelis complex. The stabilization effects of these mutations likely equally influence the energetics of both the ground state and the transition state of the catalytic reaction, leading to the unaltered kcat. Our study provides new insights into the role of conformational dynamics in glycosyltransferase’s function and new modality to modulate enzymatic efficiency.
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Affiliation(s)
- Carlos A. Ramirez-Mondragon
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
| | - Megin E. Nguyen
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Bakar A. Hassan
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Frank J. Tucci
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Ramaiah Muthyala
- Department of Experimental and Clinical Pharmacology, College Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jiali Gao
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
- Department of Chemistry, University of Minnesota, Minneapolis, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Erika A. Taylor
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
- Correspondence: (E.A.T.); (Y.Y.S.); Tel.: +1-(860)-685-2739 (E.A.T.); +1-(612)-625-6255 (Y.Y.S.); Fax: +1-(860)-685-2211 (E.A.T.); +1-(612)-625-5149 (Y.Y.S.)
| | - Yuk Y. Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (E.A.T.); (Y.Y.S.); Tel.: +1-(860)-685-2739 (E.A.T.); +1-(612)-625-6255 (Y.Y.S.); Fax: +1-(860)-685-2211 (E.A.T.); +1-(612)-625-5149 (Y.Y.S.)
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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Lu F, Zhang N, Ye T, Zhao H, Pang M, Liu SM. High throughput metabolomics-proteomics investigation on metabolic phenotype changes in rats caused by Radix Scrophulariae using ultra-performance liquid chromatography with mass spectrometry. RSC Adv 2019; 9:17791-17800. [PMID: 35520561 PMCID: PMC9064686 DOI: 10.1039/c8ra10443c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/31/2019] [Indexed: 11/21/2022] Open
Abstract
Radix Scrophulariae, a traditional Chinese herb, is used to treat various diseases, including H2O2-induced apoptosis in cardiomyocytes, HaCaT cells, hyperuricaemia, and depression. This study screened metabolites, proteins and common pathways to better understand both the therapeutic effects and side effects of this herb. Methods: Untargeted metabolomics based on UPLC-TOF-MS, coupled with proteomics based on nano-UPLC-Q-Exactive-MS/MS, were used to investigate the effects of R. Scrophulariae in rats. Fifty-one identified metabolites in urine samples and 76 modulated proteins in liver tissue were potential biomarkers for R. Scrophulariae treatment. The biomarkers and common pathways involved were steroid hormone biosynthesis, drug metabolism-cytochrome p450, drug metabolism-other enzymes, pentose and glucuronate interconversions, and starch and sucrose metabolism. Some biomarkers were beneficial for treating diseases such as cancer, tuberculosis and isovaleric acidaemia, while other biomarkers caused side effects. Metabolomic and proteomic analyses of R. Scrophulariae-treated rats provided valuable information on the biological safety and efficacy of using R. Scrophulariae clinically. Radix Scrophulariae, a traditional Chinese herb, is used to treat various diseases, including H2O2-induced apoptosis in cardiomyocytes, HaCaT cells, hyperuricaemia, and depression.![]()
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Affiliation(s)
- Fang Lu
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine Harbin P. R. China
| | - Ning Zhang
- Fist Affiliated Hospital of Guiyang University of Traditional Chinese Medicine Guizhou Guiyang P. R. China
| | - Tao Ye
- Fist Affiliated Hospital of Guiyang University of Traditional Chinese Medicine Guizhou Guiyang P. R. China
| | - Hongwei Zhao
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine Harbin P. R. China
| | - Mu Pang
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine Harbin P. R. China
| | - Shu-Min Liu
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine Harbin P. R. China.,Drug Safety Evaluation Center, Heilongjiang University of Chinese Medicine He Ping Road 24 Harbin 150040 P. R. China +86 45182193278 +86 45182193278
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